Theses and Dissertations from UMD
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Item AB INITIO MODELING OF THE SELECTIVITY AND REACTIVITY OF BOTH THERMAL AND LIGHT MEDIATED ORGANIC AND ORGANOMETALLIC TRANSFORMATIONS(2022) Dykstraa, Ryan Henry; Gutierrez, Osvaldo; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The mechanism of a reaction is the collection of events that take place that lead to the products of a chemical transformation. Though there are some events in a chemical reaction that can be observed by experiment, such long-lived intermediates, many of the events are too short lived to be measured. Due to these restrictions and the advancements in the development of moderately scaling computational tools, it is becoming commonplace to use quantum mechanical software packages to model the mechanism of a reaction. Here, I used quantum mechanical calculations alongside experimental evidence provided by multiple collaborators to understand the reactivity of both heat- and light-mediated organic transformations. In chapter 2, I investigated the role of electron donor-acceptor complexes in the generation of alkyl and acyl radicals in the presence of visible light. In addition, the pathways to the experimentally observed products, alkyl and acyl thioethers, were modeled. The lowest energy pathway to product, post-radical generation, was radical addition to the radical electron donor-acceptor complex. For a photoredox-catalyzed method to cyclopropanes from a novel halomethyl radical precursor (Chapter 3), computations strongly supported a redox-neutral reductive radical/polar crossover mechanism over radical pathways, consistent with experimental trends. Investigation of the isomerization of cinnamyl chloride to cyclopropane via a commonly used photoredox catalyst (Chapter 4) revealed that the reaction was mediated via dexter energy transfer between photocatalyst and substrate over the more commonly proposed electron transfer, affording diastereoselective product formation. A dual nickel/photoredox-catalyzed coupling of sulfinate salts and aryl halides gave a mixture of aryl sulfide and aryl sulfone products (Chapter 5), suggesting that disproportionation of sulfone radical was leading to the formation of thiyl radical. Modeling the product determining steps indicated that the product distribution was controlled by radical addition of the thiyl radical to the nickel(II) species versus reductive elimination of the sulfone bound to the nickel(III) catalyst. A bicyclo[1.1.1]pentane diborylated with pinacolboryl groups, one at the arm and head position, was found to have reactivity only at the bridgehead position (Chapter 6). Calculations of a hydrozone coupling reaction performed by the Qin group found that the reactivity was due to the unique hybridization of the bridgehead position as well as increased steric interactions at the arm position. Finally, a sulfoxide synthesized from a sulfinate salt could be activated with Grignard reagent, affording coupling of the substituents originally bound to the sulfoxide. DFT calculations validated the role of the sulfurane intermediate acting as a mediator to the coupled product.Item Mechanistic Studies of Photochemical Reactions: Photoacid Generators, Photoreleaseable Protecting Groups, and Diarylnitrenium Ions(2021) Zeppuhar, Andrea; Falvey, Daniel E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of light to drive chemical reactions is becoming increasingly popular due to the enhanced spatial and temporal control provided. Because of this, it is important to understand how these photochemical transformations occur from a mechanistic viewpoint in order to aid in the improvement of existing systems as well as in the development of new systems. The work presented in this dissertation will examine the mechanisms of several photochemical systems including photoacid generators, photoreleaseable protecting groups, and diarylnitrenium ions. Chapter 1 will begin with an introduction to organic photochemistry and describe some of the excited state reactions that will be encountered throughout this text. It will also describe laser flash photolysis, a technique critical to studying the reactive intermediates generated in photochemical reactions. Chapter 2 will describe the design and synthesis of photoacid generators that are activated via sequential two-photon absorption. The experiments conducted support a mechanism involving triplet re-excitation providing a more favorable bond scission. Chapter 3 will explore the applications of these newly developed photoacid generators, specifically for photopolymerization. It is shown that these compounds are capable of initiating both cationic and radical polymerizations depending on the intensity of visible light irradiation used. Chapter 4 will examine the 9-phenyl-9-tritylone photoreleaseable protecting group for alcohols to understand the details of its release mechanism. It is shown that the tritylone anion radical is required for alcohol photorelease. Chapters 5 and 6 will explore the behavior of diarylnitrenium ions in aqueous media. Chapter 5 will examine the reactivity of diarylnitrenium ions toward guanosine and it is shown that there is a rapid reaction to generate the C8 adduct, suggesting potential carcinogenicity. Chapter 6 will examine the reactivity of diarylnitrenium ions under acidic aqueous conditions. Under these conditions, a long-lived species is formed, and the experiments conducted indicate this species is the cation radical derived from the diarylnitrenium ion. Mechanistic analysis supports formation via a pathway separate from the nitrenium ion, suggestive of a triplet mechanism.Item Applications of Photoinduced Electron Transfer Chemistry: Photoremovable Protecting Groups and Carbon Dioxide Conversion(2016) Denning, Derek Michael; Falvey, Daniel; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Traditional organic chemistry has long been dominated by ground state thermal reactions. The alternative to this is excited state chemistry, which uses light to drive chemical transformations. There is considerable interest in using this clean renewable energy source due to concerns surrounding the combustion byproducts associated with the consumption of fossil fuels. The work presented in this text will focus on the use of light (both ultraviolet and visible) for the following quantitative chemical transformations: (1) the release of compounds containing carboxylic acid and alcohol functional groups and (2) the conversion of carbon dioxide into other useable chemicals. Chapters 1-3 will introduce and explore the use of photoremovable protecting groups (PPGs) for the spatiotemporal control of molecular concentrations. Two new PPGs are discussed, the 2,2,2-tribromoethoxy group for the protection of carboxylic acids and the 9-phenyl-9-tritylone group for the protection of alcohols. Fundamental interest in the factors that affect C–X bond breaking has driven the work presented in this text for the release of carboxylic acid substrates. Product analysis from the UV photolysis of 2,2,2-tribromoethyl-(2′-phenylacetate) in various solvents results in the formation of H–atom abstraction products as well as the release of phenylacetic acid. The deprotection of alcohols is realized through the use of UV or visible light photolysis of 9-phenyl-9-tritylone ethers. Central to this study is the use of photoinduced electron transfer chemistry for the generation of ion diradicals capable of undergoing bond-breaking chemistry leading to the release of the alcohol substrates. Chapters 4 and 5 will explore the use of N-heterocyclic carbenes (NHCs) as a catalyst for the photochemical reduction of carbon dioxide. Previous experiments have demonstrated that NHCs can add to CO2 to form stable zwitterionic species known as N-heterocylic-2-carboxylates (NHC–CO2). Work presented in this text illustrate that the stability of these species is highly dependent on solvent polarity, consistent with a lengthening of the imidazolium to carbon dioxide bond (CNHC–CCO2). Furthermore, these adducts interact with excited state electron donors resulting in the generation of ion diradicals capable of converting carbon dioxide into formic acid.Item Making Sense of 2D Diagrams: Examining How Models and Modeling Impact Novice Students' Development of Representational Competence in Organic Chemistry(2013) Olimpo, Jeffrey T.; Hyler, Maria; Curriculum and Instruction; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In the field of chemistry, representations serve an essential function in conveying and communicating knowledge about the chemical world. While experts are traditionally adept at identifying, interpreting, and manipulating these visualizations, novices often are not. To address the concern of promoting representational competence in novice populations, the series of studies presented in this dissertation utilizes a mixed-methods approach to examine the relationship between students' use of concrete models and their performance, specifically, on representational translation tasks (RTTs) in Organic Chemistry. Students' perceptions of modeling and faculty perceptions of and uses of models in classroom contexts are also examined. While results indicated significant increases in performance on RTTs for students who made effective use of concrete models to complete these tasks, students' proclivity for using models was found to be negatively influenced, at times, by perceived practical constraints of the learning environment -modeling being too time-consuming of a task, no engagement in modeling practices in the classroom or directed instruction on how to build and use models, etc. In addition, while faculty were generally found to view models in a positive light, classroom observation data revealed that their use of models during instruction was often inconsistent with promoting representational competence. Together, these data suggest that attention to both cognitive and contextual factors need be taken into consideration when attempting to create a holistic account of how novices come to develop representational competence in the domain.Item The synthesis of a diverse library of AI-2 analogs to investigate bacterial quorum sensing(2011) Smith, Jacqueline A.; Sintim, Herman O; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Bacteria have evolved several mechanisms to promote their survival, which sometimes come at the cost of human health. They use toxins known as virulence factors to cause the symptoms associated with infections. They also form communities called biofilm, which allow them to thrive and resist attacks by the host's immune system. Conventional antibiotics fail to penetrate the biofilm matrix. The expression of virulence factors and formation of biofilm are both regulated by a phenomenon known as quorum sensing. Quorum sensing is a form of cell-to-cell communication, which allows bacteria to coordinate gene expression via the secretion of signaling molecules, known as autoinducers, and the subsequent detection of these molecules. The ultimate goal of this dissertation was to identify new small molecules that would be used to disrupt quorum sensing in bacteria. AI-2, which is a universal quorum sensing autoinducer, found in over 60 bacterial species, was targeted. In this study a new facile synthesis of AI-2 was achieved and this new methodology was adapted to the synthesis of a library of analogs. These analogs were screened for their ability to modulate AI-2 mediated quorum sensing in Vibrio harveyi, Escherichia coli, Salmonella typhimurium and Pseudomonas aeruginosa. It was found that AI-2 analogs were able to cause synergistic agonism of bioluminescence in V. harveyi. Furthermore, several analogs were able to repress quorum sensing in E. coli yet very few analogs were active in the homologous quorum sensing system of S. typhimurium. These analogs were processed by the AI-2 processing enzymes in E. coli. Finally some AI-2 analogs were found to inhibit quorum sensing in P. aeruginosa in pure culture as well as in mixed cultures. These findings will provide the framework for the development of new small molecules which are able to modulate quorum sensing and thus act as tools in the inhibition of bacterial virulence and biofilm formation.Item Acyclic Congeners of Cucurbit[n]uril and a Related Mechanistic Study on the Cucurbit[n]uril Forming Reaction.(2010) Ma, Da; Isaacs, Lyle D; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Supramolecular chemistry has been a very important research area in the past several decades. In this research field, molecular containers, such as cyclodextrin, attracts special attention due to their wide applications both in academia and industry. Cucurbit[n]uril (CB[n]), as a new generation molecular container, has selective and tight binding towards lots of cations and neutral molecules. A homologous family of CB[n] has been discovered including CB[5]-CB[8], CB[10], iCB[n], ns-CB[10] and ns-CB[6]. CB[n] analogues and derivatives have also been developed. CB[n] still has several issues, such as low solubility in water, difficulty to be functionalized, and slow association and dissociation kinetics. This thesis describes efforts to address these issues by developing new CB[n] type molecular containers and carrying out mechanistic investigations. Three chapters are included in this thesis. Chapter 1 is a literature review of molecular encapsulation and molecular container chemistry. We first introduced general concepts of molecular encapsulation and present examples of molecular container, such as cyclodextrin. This is followed by an introduction to CB[n] molecular containers and their supramolecular chemistry. Chapter 2 introduces new acyclic CB[n] congeners II-5a and II-5b. II-5a and II-5b are obtained from step-wise synthesis with reasonable yields. This step-wise synthetic route avoids difficult separation process. We measured the binding constants of II-5a towards a number of guests and found the binding affinity is usually comparable to CB[7]. The recognition property of II-5a is investigated in depth. We found that the length and functional groups of the guests greatly influence the binding affinity. Nevertheless, the charge and size of the guests do not have as a big influence on the binding constants as CB[7]. We discovered that the ionic strength of the buffer is critical for the binding constant. By comparing the recognition property of II-5a and II-6, it is discovered that the substituted o-xylyene walls are important for the tight binding compounds. II-5a and II-5b are new examples of CB[n] type molecular containers. They retain most of the good recognition property of CB[n] and have advantages compared to CB[n], including 1) aromatic walls that makes further functionalization possible; 2) acyclic structure that enables fast association and dissociation kinetics. Chapter 3 describes the mechanistic study of CB[n] forming reactions. Another possible way to synthesize CB[n] molecular container is to use aldehydes instead of paraformaldehyde. But neither previous researchers nor our work has succeeded to make the aldehydes participating CB[n] forming reactions happen. Mechanistic investigation was carried out to explain why this reaction simply does not occur. We used III-7 instead of glycoluril to avoid cyclization reactions. Several reasons are discovered: 1) side products are formed, such as III-SP1 and III-SP2; 2) S-shape intermediates are yielded, such as III-15S, III-16S, III-17S and III-18S, which are not able to continue the reaction to form macrocycles; 3) a small equilibrium constant for the chain grouth reaction. This study explains why aldehydes usually do not participate in CB[n] forming reactions. This work could also lead to the discovery of certain aldehydes that can form CB[n] type macrocycles.